Granulomatosis with polyangiitis is a life-threatening systemic vasculitis, characterised by anti-neutrophil cytoplasmic autoantibodies (ANCA) most commonly against proteinase 3 (PR3), a protease expressed intracellularl...Granulomatosis with polyangiitis is a life-threatening systemic vasculitis, characterised by anti-neutrophil cytoplasmic autoantibodies (ANCA) most commonly against proteinase 3 (PR3), a protease expressed intracellularly and on the surface of neutrophils. Most cell surface PR3 is bound to the receptor CD177; however, the molecular mechanism of the interactions is not well understood. Here, we present crystal structures of CD177 in complex with PR3 and unliganded CD177. We describe a mainly hydrophobic binding interface between PR3 and CD177, involving the first two Ly6/uPAR (LU) domains of CD177. These form a globular structure which is connected to downstream domains via a flexible linker. Using a panel of PR3-ANCA-positive patient samples, we show that a significant proportion of ANCAs target the CD177-binding site of PR3 in these samples. Structure-guided mutation of the CD177-binding site on PR3 is effective in reducing PR3-ANCA binding. The results demonstrate that the CD177-binding surface of PR3 harbours a major PR3-ANCA epitope, and that the extent of binding to this surface varies between different patients.
Functional defects resulting from deleterious mutations can often be restored during evolution by compensatory mutations. Importantly, this process can generate the genetic diversity seen in networks regulating the same...Functional defects resulting from deleterious mutations can often be restored during evolution by compensatory mutations. Importantly, this process can generate the genetic diversity seen in networks regulating the same biological function in different species. How the options for compensatory evolution depend on the molecular interactions underlying these functions is currently unclear. We investigate how gene deletions compensating for a defect in the polarity pathway of Saccharomyces cerevisiae impact the fitness landscape. Using a transposon mutagenesis screen, we demonstrate that gene disruption tolerance has changed on a genome-wide scale in the compensated strain. An analysis of the functional associations between the affected genes reveals that compensation impacts cellular processes that have no clear connection to cell polarity. Moreover, genes belonging to the same process tend to show the same direction of tolerance change, indicating that compensation rewires the fitness contribution of cellular processes rather than of individual genes. In conclusion, our results strongly suggest that functional overlap between modules and the interconnectedness of the molecular interaction network play major roles in mediating compensatory evolution.
Eukaryotic chromosome segregation requires attachment of chromosomes to microtubules through the kinetochore so that chromosomes can align and move in mitosis. Kinetochores assemble on the centromere, which is epigenetic...Eukaryotic chromosome segregation requires attachment of chromosomes to microtubules through the kinetochore so that chromosomes can align and move in mitosis. Kinetochores assemble on the centromere, which is epigenetically defined by the histone H3 variant CENtromere Protein A (CENP-A). During DNA replication, CENP-A is equally divided between replicated chromatids, and new CENP-A nucleosomes are re-assembled during the subsequent G1 phase. How cells regulate the cell cycle timing of CENP-A assembly is a central question in the epigenetic maintenance of centromeres. CENP-A nucleosome assembly requires the Mis18 complex (Mis18α, Mis18β, and M18BP1), whose localization to centromeres occurs between metaphase and G1. Here, we define a new regulatory mechanism that works through phosphorylation of Xenopus laevis M18BP1 between metaphase and interphase. Phosphorylation disrupts binding of M18BP1 to CENP-A nucleosomes in metaphase, and when relieved, enables M18BP1 binding to CENP-A nucleosomes in interphase. We show that this phosphorylation-dependent mechanism regulates CENP-A nucleosome assembly. We propose that the phospho-regulated binding of M18BP1 to CENP-A nucleosomes restricts new CENP-A assembly to interphase.
Tissue damage activates immediate responses to restrict further harm and initiate repair. How injury sensing is coupled to regeneration is still not well understood. Here, we study regenerative responses in the adult Dro...Tissue damage activates immediate responses to restrict further harm and initiate repair. How injury sensing is coupled to regeneration is still not well understood. Here, we study regenerative responses in the adult Drosophila brain, where proliferation is normally strongly restricted. We show that localized brain damage triggers oxidative stress and diverse brain protective programs. We find that ROS generation by the NADPH Oxidase Duox in glial cells is responsible for injury-induced oxidative stress. Both genetic and chemical suppression of ROS in injured brains impairs regeneration. In particular, selective knockdown of calcium-sensitive Duox in glia, which show elevated calcium after injury, reduces injury-induced proliferation. We further provide evidence that diffusing ROS can sustain the activity of pro-regenerative signaling, which is required to stimulate cell divisions. Although oxidative stress is generally considered as harmful in the brain, we uncover here an unanticipated beneficial role of transient ROS release by glia to promote brain repair.
In many animals, primordial germ cells are transiently segregated outside the somatic-cell cluster that forms the embryo's body during early embryogenesis. This physical segregation of the germline from the soma has long...In many animals, primordial germ cells are transiently segregated outside the somatic-cell cluster that forms the embryo's body during early embryogenesis. This physical segregation of the germline from the soma has long been believed to be crucial for germline development, but the mechanisms controlling this segregation and its developmental significance remain unclear. Here, in Drosophila, we show that somatic gene silencing in the germline is essential for maintaining this segregation. Primordial germ cells (pole cells) lacking the Nanos- and Polar granule component (Pgc)-dependent dual repression mechanism misexpress widespread somatic genes. They form abnormal cellular protrusions, invade adjacent somatic epithelium, and intermingle with somatic cells. These mislocalized pole cells ultimately undergo cell death, whereas properly segregated cells survive. Notably, knockdown of miranda (mira), one of the somatic genes ectopically expressed, rescues these phenotypes. Our findings uncover a previously unrecognized mechanism whereby somatic gene silencing safeguards the physical boundary between the germline and the somatic cells forming the embryo's body, highlighting its potential role in ensuring germline viability during early development.
Cell polarity is a crucial biological process essential for cell division, directed growth, and motility. In Saccharomyces cerevisiae, polarity establishment centers around the small Rho-type GTPase Cdc42, which cycles b...Cell polarity is a crucial biological process essential for cell division, directed growth, and motility. In Saccharomyces cerevisiae, polarity establishment centers around the small Rho-type GTPase Cdc42, which cycles between GTP-bound and GDP-bound states, regulated by GEFs like Cdc24 and GAPs such as Rga2. To dissect the dynamic regulation of Cdc42, we employed in vitro GTPase assays, revealing inverse concentration-dependent profiles for Cdc24 and Rga2: with increasing concentration, Cdc24's GEF activity is nonlinear and oligomerization-dependent, which is possibly linked to the relief of its self-inhibition. In contrast, Rga2's GAP activity saturates, likely due to self-inhibition upon oligomerization. Together, Cdc24 and Rga2 exhibit a strong synergy driven by weak Cdc24-Rga2 binding. We propose that the synergy stems from Cdc24 alleviating the self-inhibition of oligomeric Rga2. We believe this synergy contributes to efficient regulation of Cdc42's GTPase cycle over a wide range of cycling rates, enabling cells to resourcefully establish polarity. As Cdc42 is highly conserved among eukaryotes, we propose the GEF-GAP synergy to be a general regulatory property in other eukaryotes.
Proper regulation of ribosome biogenesis is essential for stem cell function and tissue homeostasis, yet its upstream control in adult intestinal stem cells (ISCs) remains unclear. Here, we identify the WD repeat protein...Proper regulation of ribosome biogenesis is essential for stem cell function and tissue homeostasis, yet its upstream control in adult intestinal stem cells (ISCs) remains unclear. Here, we identify the WD repeat protein Wdr4 as a key regulator of ISC homeostasis in the Drosophila midgut. Wdr4 cooperates with the methyltransferase Mettl1 to catalyze N⁷-methylguanosine (m⁷G) modification of let-7 miRNA. Wdr4 or Mettl1 depletion disrupts this modification, reducing let-7 levels and aberrantly activating TOR-JNK-dMyc signaling. This drives elevated ribosome biogenesis, ISC overproliferation, misdifferentiation, and intestinal dysplasia. Overexpression of let-7, inhibition of TOR, or suppression of JNK rescues these defects. Importantly, expression of human WDR4 and METTL1, but not catalytic-dead METTL1 mutant, restores ISC homeostasis in Wdr4- and Mettl1-depleted flies, establishing a conserved Wdr4/Mettl1-let-7-TOR-JNK axis that links miRNA modification to translational control and tissue integrity. Together, our findings uncover a previously unrecognized function of miRNA m⁷G methylation in regulating ribosome biogenesis and maintaining intestinal homeostasis.
To address the replication crisis and instill confidence in the scientific literature, we introduce a new framework for evaluating scientific manuscripts. “Peer replication” would be an alternative or augmentation to pee...To address the replication crisis and instill confidence in the scientific literature, we introduce a new framework for evaluating scientific manuscripts. “Peer replication” would be an alternative or augmentation to peer review and elevate peer-replicable works to a higher tier of publication. [Image: see text]
Bodner J, Vadlamani P, Lee AS
… +10 more, Helmin KA, Liu Q, Pratasenia AE, Horst MMA, Ravisankar S, Khurana S, Mendillo ML, Singer BD, Srivastava S, Foltz DR
Proper histone gene expression is critical for cell viability and maintenance of genomic integrity. Multiple histone genes are organized into three genomic loci that encode replication-coupled core and linker histones. H...Proper histone gene expression is critical for cell viability and maintenance of genomic integrity. Multiple histone genes are organized into three genomic loci that encode replication-coupled core and linker histones. Histone gene expression and transcript processing are orchestrated in the histone locus body (HLB) within the nucleus. Here, we identify human CRAMP1 as a selective regulator of the linker histone H1 expression. Human CRAMP1 is recruited to the HLB in RPE1 cells. Immunoprecipitation combined with mass spectrometry shows CRAMP1 physically associates with the HLB component GON4L (also known as YARP). We demonstrate that the PAH domains of GON4L interact with CRAMP1. CRAMP1 disruption results in reduced histone H1 mRNA expression and histone H1 protein levels, with no significant changes in core histone gene expression. CRAMP1 occupies the promoters of actively expressed replication-coupled linker histone genes that reside within the histone locus body and replication-independent histone H1 loci, which reside in a region of the genome without other histone genes. Together, these data identify CRAMP1 as a novel and selective regulator of histone H1 gene expression.
Large language models can defend a hypothesis and its opposite with equal eloquence, raising a new risk for scientific reasoning: confusing rhetorical plausibility with evidential support. This essay analyzes how LLMs re...Large language models can defend a hypothesis and its opposite with equal eloquence, raising a new risk for scientific reasoning: confusing rhetorical plausibility with evidential support. This essay analyzes how LLMs reshape creativity, judgment and responsibility in research—and how scientists can engage their fluency without surrendering epistemic discipline. [Image: see text]
Arbi M, Skamnelou M, Koufoudaki L
… +14 more, Bakali V, Bournaka S, Zitouni S, Tsaridou S, Karayel O, Vasilopoulou CG, Tsika AC, Giakoumakis NN, Preza O, Spyroulias GA, Mann M, Bettencourt-Dias M, Taraviras S, Lygerou Z
The centriole duplication cycle must be tightly controlled and coordinated with the chromosome cycle. Aberrations in centriole biogenesis can cause developmental disorders, ciliopathies and cancer, yet the molecular dete...The centriole duplication cycle must be tightly controlled and coordinated with the chromosome cycle. Aberrations in centriole biogenesis can cause developmental disorders, ciliopathies and cancer, yet the molecular determinants controlling centriole numbers and the link between the two cycles remain poorly characterized. Here, we demonstrate that McIdas, previously implicated in cell cycle regulation and multiciliogenesis, plays a critical role in maintaining proper centriole numbers. McIdas localizes to centrioles, where it exhibits dynamic localization throughout the cell cycle, dependent upon a nuclear export signal (NES) in its coiled-coil domain. Overexpression of McIdas induces centriole overduplication, whereas its depletion perturbs daughter centriole biogenesis and SAS6 recruitment. An NES mutant of McIdas that fails to localize to centrioles does not induce centriole amplification. Moreover, McIdas depletion reduces PLK4-induced centriole amplification. McIdas interacts with and is phosphorylated by PLK4, which is critical for its role in centriole number control. Overall, our results demonstrate that in addition to its known nuclear localization, McIdas also localizes to centrioles, affecting centriole duplication. This novel, direct role of McIdas in centriole duplication connects its functions in cell cycle regulation and multiciliogenesis.
The Drosophila Toll/NF-κB pathway has been extensively studied for its roles in innate immunity and embryonic development. Nevertheless, the regulatory mechanisms underlying Spz/Toll signaling in non-immune contexts rema...The Drosophila Toll/NF-κB pathway has been extensively studied for its roles in innate immunity and embryonic development. Nevertheless, the regulatory mechanisms underlying Spz/Toll signaling in non-immune contexts remain poorly understood. Here, we demonstrate a critical role for Toll in regulating intestinal stem cell activity through direct transcriptional control of PI3K and Akt in an insulin-independent manner. Time-series transcriptomic analysis of intestinal damage and repair responses reveals that the stress-responsive factor Jumu regulates Spz expression to activate Toll signaling. Disruption of the Jumu/Spz/Toll cascade or PI3K/Akt signaling impairs intestinal regeneration and suppresses tumor growth, and epistasis analysis confirms that PI3K/Akt functions downstream of Toll. Our findings elucidate an autocrine Spz/Toll-mediated mechanism that drives stem cell function via the PI3K/Akt pathway during tissue homeostasis and uncover a critical non-immune role of Toll signaling in both physiological and pathological contexts.
Cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS) is a critical cytosolic DNA sensor, whose activity can be regulated by acetylation. Here, we show that nicotinamide adenine dinucleotide (NAD)-dependent lysine dea...Cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS) is a critical cytosolic DNA sensor, whose activity can be regulated by acetylation. Here, we show that nicotinamide adenine dinucleotide (NAD)-dependent lysine deacetylase SIRT4 interacts with cGAS and positively regulates innate immune responses triggered by DNA viruses or cytoplasmic DNA. Overexpression of SIRT4 inhibits HSV-1 infection, whereas knockdown of SIRT4 has the opposite effect. Deficiency of SIRT4, or treatment with a SIRT4 inhibitor, impairs antiviral innate immune signaling in response to DNA viruses or cytoplasmic DNA, both in vitro and in vivo. Moreover, SIRT4 inhibitor treatment attenuates type I interferon signaling in Trex1-deficient cells and in peripheral blood mononuclear cells (PBMCs) from patients with systemic lupus erythematosus (SLE). Mechanistically, SIRT4 deacetylates cGAS and enhances its association with double‑stranded DNA. Collectively, our study identifies SIRT4 as a positive regulator of cGAS-mediated innate immune signaling pathways, which advances the understanding of the regulation of cGAS activity.
The peer review process is fundamental to scientific validation, yet ownership and permitted uses of the resulting content remain insufficiently defined. To ensure the future integrity and impartiality of manuscript asse...The peer review process is fundamental to scientific validation, yet ownership and permitted uses of the resulting content remain insufficiently defined. To ensure the future integrity and impartiality of manuscript assessment, journals must consider updating community agreements that define the reuse rights of reviewers and establish mechanisms for consent or compensation. [Image: see text]
The transmembrane protein CMTM6 promotes plasma membrane expression of the immune checkpoint protein PD-L1, a key suppressor of anti-tumor immunity. Targeting CMTM6 has been proposed as a strategy to enhance tumor cell k...The transmembrane protein CMTM6 promotes plasma membrane expression of the immune checkpoint protein PD-L1, a key suppressor of anti-tumor immunity. Targeting CMTM6 has been proposed as a strategy to enhance tumor cell killing by reducing PD-L1 surface expression. In accord, ablation of CMTM6 in mouse cancer models was shown to efficiently suppress tumor growth, but unexpectedly in a manner partially independent of PD-L1, suggesting that CMTM6 may regulate additional proteins involved in anti-tumor immunity. Using mass spectrometry, we discovered that mouse CMTM6 strongly associates with the cell death receptor FAS and negatively regulates its surface expression in mice. Deletion of CMTM6 increases FAS plasma membrane localization and sensitizes murine cells to FAS ligand-induced cytotoxicity. However, the interaction between CMTM6 and FAS is absent in human cells due to the difference in three amino acids at the boundary of the FAS extracellular and transmembrane domains. Altogether, our findings urge caution when translating promising data regarding the targeting of CMTM6 from mouse cancer models to potential human therapies.
Cell fate decisions in the early embryo rely on reciprocal transcriptional networks that balance pluripotency with lineage commitment. NANOG is essential for directing the epiblast-primitive endoderm (PrE) fate choice, b...Cell fate decisions in the early embryo rely on reciprocal transcriptional networks that balance pluripotency with lineage commitment. NANOG is essential for directing the epiblast-primitive endoderm (PrE) fate choice, but the molecular mechanisms underlying its repressive activity remain incompletely understood. Here we show that NANOG partners with TBX3 and the PRC2 complex to maintain embryonic stem cell (ESC) identity by silencing PrE genes through newly identified distal enhancers. Loss of Nanog reduces PRC2-mediated repression of Gata6, initiating its expression independently of TBX3. Subsequent TBX3 upregulation enables its association with GATA6, driving a feed-forward programme that activates Gata6, Gata4 and Sox17 and promotes PrE differentiation. Thus, NANOG suppresses PrE fate not only by direct repression but also by preventing TBX3 from switching partners. These findings define a Nanog-Tbx3-Gata6 regulatory axis that integrates enhancer control, chromatin regulation and transcription factor redeployment to couple ESC maintenance with lineage commitment.
Intrinsically disordered regions (IDRs) are widespread in proteins, yet their evolutionary paths remain poorly understood. Using galectin, a universal carbohydrate-binding protein, we investigated how IDRs evolved and ac...Intrinsically disordered regions (IDRs) are widespread in proteins, yet their evolutionary paths remain poorly understood. Using galectin, a universal carbohydrate-binding protein, we investigated how IDRs evolved and acquired their biological roles in vertebrates. Through extensive proteome-wide sequence analyses, we found that vertebrate galectin IDRs share overall amino acid compositions but differ significantly in their aromatic residue types. Using nuclear magnetic resonance (NMR) spectroscopy and lipopolysaccharide micelle assays, we demonstrated that despite these differences, IDRs from various vertebrate galectins independently converged toward a similar function: mediating agglutination via phase separation. Our data suggest that the specific types of aromatic residues within these IDRs were established early in evolution and underwent independent expansions among different vertebrate lineages. Additionally, we identified a conserved short N-terminal motif critical for promoting galectin self-association, which likely served as an incipient sequence for subsequent IDR evolution. Contrary to previous peptide studies emphasizing aromatic residue specificity, our findings highlight the evolutionary preference for increasing motif repetition over residue-type optimization to achieve functional fitness.
Zhang H, Wang Z, Wang X
… +22 more, Yu W, Zhang G, Zhang H, Lu Y, Sun Y, Lu T, Li X, Yang R, Sun J, Xu J, Huang S, Ma X, Ren J, Tang N, Cheng Z, Yu J, Wei F, Zhou H, Li J, Qin J, Jin Y, Zhang L
Paneth cells are defensive cells in the intestinal tract, which secrete niche factors and antimicrobial peptides (AMPs) to maintain the small intestinal stem cell niche and immune homeostasis. Here, we show that Vestigia...Paneth cells are defensive cells in the intestinal tract, which secrete niche factors and antimicrobial peptides (AMPs) to maintain the small intestinal stem cell niche and immune homeostasis. Here, we show that Vestigial-like family member 4 (VGLL4) plays a pivotal role in maintaining small intestinal homeostasis and in regulating Paneth cells. VGLL4 expression is downregulated in response to irradiation and DSS-induced colitis. Consistently, public datasets of human colitis show reduced VGLL4 expression. Loss of VGLL4 in the intestinal epithelium decreases Paneth cell numbers and AMPs production, and triggers gut microbiota dysbiosis, impairing intestinal regenerative capacity. Mechanistically, VGLL4 forms a complex with TEAD4 and ATOH1, stimulating GFI1 expression and promoting Paneth cell differentiation. Furthermore, VGLL4 forms a complex with TEAD4 and TCF4 to induce defensin expression, thereby maintaining microbiota composition. Collectively, our findings uncover novel roles for VGLL4 in intestinal homeostasis.
Liu L, Massey EJ, Zuo D
… +14 more, Pacis A, Demirdizen M, Podleszanski E, Cinkornpumin J, Gu Y, Proud H, Sanguin-Gendreau V, Papavasiliou V, Hossain I, Jiang Z, Smith HW, Pastor WA, Ceppi P, Muller WJ
Breast cancer remains a leading cause of death among women, with the HER2+ subtype being particularly aggressive due to acquired resistance to HER2-targeted therapies. Enhancer of Zeste Homolog 2 (EZH2), the catalytic su...Breast cancer remains a leading cause of death among women, with the HER2+ subtype being particularly aggressive due to acquired resistance to HER2-targeted therapies. Enhancer of Zeste Homolog 2 (EZH2), the catalytic subunit of Polycomb Repressive Complex 2, represses the expression of genetic programs crucial for differentiation, proliferation, and apoptosis. To investigate the role of EZH2 in HER2+ tumor progression, we crossed a genetically engineered mouse model of HER2-driven breast cancer with a conditional Ezh2 knockout strain and showed that Ezh2 is essential for accelerating tumor initiation and metastatic dissemination. Combined bulk and single cell RNA sequencing analyses revealed a significant downregulation of basal cell populations in the absence of Ezh2, and an upregulation of luminal progenitor cell populations, driven by crucial transcription factors such as Esr1. Further, inhibition of EZH2 in vitro resulted in increased expression of ER in HER2+ human breast cancer cell lines and conferred sensitivity to Tamoxifen. These findings demonstrate that EZH2 dictates cancer plasticity and provides rationale for combining EZH2 inhibitors with endocrine therapies to improve HER2+ breast cancer outcomes.
Cornut M, Djebali S, Rondeau E
… +17 more, Dayet S, Fayolle T, Haagen J, Fallone L, Rousseaux N, Caspar E, Marcotte M, Martin A, Courteboeuf E, Deschamps-Biboulet M, Teixeira M, Marvel J, Py BF, Walzer T, Marcais A, Henry T, Bourdonnay É
IRF2 plays an indirect role in inflammasome activation by regulating Caspase-4 and Gasdermin D (GSDMD) levels. However, the in vivo relevance of this regulatory circuit is unknown. We generate IRF2 mice and demonstrate t...IRF2 plays an indirect role in inflammasome activation by regulating Caspase-4 and Gasdermin D (GSDMD) levels. However, the in vivo relevance of this regulatory circuit is unknown. We generate IRF2 mice and demonstrate that they are equally susceptible to Francisella novicida infection as GSDMD mice. Interestingly, the phenotypes of IRF2 and GSDMD mice diverge with respect to IFN-γ. Specifically, IRF2 mice exhibit a profound defect in IFN-γ production, which we attribute to an intrinsic role of IRF2 in regulating both the number and maturation of NK cells. IRF2 NK cells fail to express the antibacterial effectors IL-18R and Granzyme A, thereby impairing bacterial clearance. IFN-γ therapy partially restores immune responses in IRF2 mice and resistance to infection. These findings confirm IRF2 as a dual regulator of inflammasome activity and NK cell function, highlighting its pivotal role in innate immunity. Moreover, they underscore the potential of IFN-γ therapy as a promising treatment for severe infections in patients with primary immunodeficiencies affecting multiple immune pathways.